Usher bug on JN.1.16.1+S:L456V/JN.1.18+S:R346K

[xz-keg]

JN.1.16 is JN.1+S:F456L(T22928C)+S:R346T, and there is an S:L456V(C22928G) branch under it.

Given it is a single-nuc mutation on 22928, it is very unlikely for this position to mutate so frequently, a better explanation shall be
JN.1.18(JN.1+S:R346T)+S:F456V(T22928G).

Seems that this is something related to the fundamental algorithm of usher, we previously see this bug in HK.1.1(retracted) too, where usher categorizes EG.5.1.1+S:G257D+S:L455F seqs as EG.5.1.1+S:G257V+S:L455F+S:V257D.

@AngieHinrichs

[xz-keg]

@corneliusroemer I see the 2 seqs of S:F456V also included in JN.1.16.1-defining seqs. Please remove them.

[FedeGueli]

JN.1.16 is JN.1+S:F456L(T22928C)+S:R346T, and there is an S:L456V(C22928G) branch under it.

Given it is a single-nuc mutation on 22928, it is very unlikely for this position to mutate so frequently, a better explanation shall be JN.1.18(JN.1+S:R346T)+S:F456V(T22928G).

Seems that this is something related to the fundamental algorithm of usher, we previously see this bug in HK.1.1(retracted) too, where usher categorizes EG.5.1.1+S:G257D+S:L455F seqs as EG.5.1.1+S:G257V+S:L455F+S:V257D.

@AngieHinrichs
the two samples in JN.1.18 have also A6705G that is a branch of Jn.1.18 so likely it is not the same lineage even if they share Bangladesh as country of emergence

[xz-keg]

There is another example of this bug for JN.1.18+G17562T+S:T346K. (Shall be JN.1+G17562T+S:R346K)

[Over-There-Is]

I think "HK.1.1" is from the mergence of HK.1+S:L455F and misplaced HK.3+S:G257D by usher.

[FedeGueli]

@AngieHinrichs has this one been solved ?

[AngieHinrichs]

Not yet but I will try to get to the accumulated issues tonight.

@aviczhl2 @Over-There-Is When reporting a problem with the tree, it would be very helpful if you could give a sequence name or ID from the base of the branch that you believe is misplaced, so that I can be sure I know what branch you're talking about.

For example, in this case I think you're referring to the branch with BGD/9850683/2024 (PP301390.1) as the branch that should be moved to JN.1.18.

But regarding JN.1+G17562T+S:R346K, I don't see a branch with both of those mutations. There is now a JN.1 > S:R346K (G22599A) branch e.g. USA/AZ-CDC-QDX92152836/2024 (PP349116.1) but it doesn't have any sequences with G17562T. I don't see a JN.1 > G17562T branch (there is a BA.2.86.1 > ... > G17562T e.g. USA/PA-CDC-LC1086705/2024 PP189111.1).

[AngieHinrichs]

I did a force-move of the branch with BGD/9850683/2024 to JN.1.18 a couple days ago and so far matOptimize has left it there. 🤞